[gmx-users] mdrun -multi
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Mon Dec 1 17:08:01 CET 2003
> > I would like to run mdrun with the option -multi (multiple simulations in
> > paralell). Suppose that I have 4 nodes (8cpus), is it possible to run 8
> > simulations in parallel on these 8cpus?
> AFAIK there is one, and only one!, sensible reason for using mdrun -multi
> and that is when you have access to a supercomputer with rather strict
> policies on the queues. That is, many supercomputer administrators require
> that only parallel (and thus multi-processor) jobs can be run. If, in stead,
> you have a (large) number of individual simulations that you want to run
> you can use mdrun -multi to bypass this queuing policy by making the system
> think you are running a paralell job, while you actually run multiple
> independent simulations.
> In all other cases, IMHO, you should simply start multiple separate instances
> of mdrun!
thanks Anton. Here we have a linux cluster with many queues but each
queues has only 2 cpus. If I use mdrun -np 4 -multi then four jobs will be
submitted to one queue and running on 2cpus. Are there possibilities
(some trick or modify the code) to distribute these 4 jobs on 4
cpus (2 queues)? Of course without starting multiple separate
instances of mdrun.
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